Deviations from Hardy-Weinberg equilibrium

shinkenshinken IrapuatoMember ✭
in Ask the GATK team

Hi,

I have a mix of heterozygous (3 samples) and inbreed samples (5 samples). I am wondering how could affect to make the SNP calling without taking into account deviations from Hardy-Weinberg equilibrium. How could I take into account these using GATK?

Best Wishes,

Eric

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  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @shinken
    Hi Eric,

    What exactly is your end goal? If you use joint-genotyping, the genotypes will not be affected. The only annotations I can think of that would be affected are InbreedingCoeff and ExcessHet.

    -Sheila

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  • shinkenshinken IrapuatoMember ✭

    ok,

    The problem that I am having is a very low SNP calling in inbred lines that are also low coverage lines (4x). I was wondering if the problem could be, in addition to the low coverage, the filters about deviations from the HW equilibrium.

    I am calling this SNPs together with heterozygous samples (30x coverage) and I am not having problems with those ones. Do you think that the only problem is the coverage? Maybe sounds silly but using other programs such as ANGSD to obtain the genotypes I am not having this really low SNP calling in the low-coverage samples. So, I am trying to figure out what is happening.

    Thank you.

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